If you could link me to a scholarly article that describes how after endosymbiosis, the bacterial cell and it's eukaryotic host coordinated replication (or if you can explain it to me yourself) I would be really grateful. Originally, they replicated separately, so I'm not sure how they stayed together through generations. Was there some sort of chemical messenger that the mitochondria of a cell received to know it was time to replicate? I don't know. Science help.

There must be some synchronization cues; otherwise many cells would end up with over- or under-optimal numbers of mitochondria. Since many of the critical proteins in a mitochondrian are nuclear-encoded, the proliferation of the mitochondria can be limited by the availability of the nuclear-encoded gene products. It would be interesting if there are faster linkages, such as signaling cascades, the trigger mitochondrial replication checkpoints. I'm speculating; has anyone looked into the literature on this?

According to the endosymbiontic theory mitochondria were ancient bacteria that survived in an ancient eukaryotic cell and continued to live as part of it as an organelle. So, I suppose, in any eukaryotic cell the mtDNA should be relatively conserved. However, the mutational rate of mtDNA is ten fold higher than that of nuclear DNA. So is the mtDNA sequence conserved among e.g. various mammalian species or the opposite?

Another question about mtDNA: what is the advantage to/role of having multiple copies of the same circular DNA molecule? Isn't that "too much of a dose" of the same given gene? Any mitochondria expert out here?

Regarding the regulation of replication of mitochondria, this paper discusses an influence of tumor necrosis factor alpha on mitochondrial replication while exploring the effect of adenosine on that regulatory system.